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Search took 0.01 seconds. Search: Posts Made By: kopi-o
Forum: Bioinformatics 02-05-2015, 03:07 AM
Replies: 9
Views: 5,818
Posted By kopi-o
This has code for going between RPKM and TPM (and...

This has code for going between RPKM and TPM (and also effective counts)

https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/

A very nice post.
...
Forum: Bioinformatics 01-30-2015, 02:59 AM
Replies: 5
Views: 2,747
Posted By kopi-o
Yes. Since the prep was not strand-specific, your...

Yes. Since the prep was not strand-specific, your contig's orientation is arbitrary.
Forum: RNA Sequencing 10-10-2014, 02:42 PM
Replies: 3
Views: 1,350
Posted By kopi-o
It may be sufficient - after all, you have quite...

It may be sufficient - after all, you have quite a few samples. With a small number of samples it can be hard to achieve the necessary statistical power without "borrowing variance across genes".
...
Forum: RNA Sequencing 10-10-2014, 12:02 AM
Replies: 11
Views: 3,041
Posted By kopi-o
In my opinion, CuffDiff2 is just overly...

In my opinion, CuffDiff2 is just overly conservative. I have seen this type of counter-intuitive result often. I would put more trust in DESeq2 / edgeR / limma. Also, just about all DE analysis...
Forum: RNA Sequencing 09-26-2014, 12:39 AM
Replies: 5
Views: 3,417
Posted By kopi-o
This line looks like your answer: Warning:...

This line looks like your answer:

Warning: Same mate file "A_1_C4HUHACXX_AGTCAA_L003_R1.fastq" appears as argument to both -1 and -2

You have put A_1_C4HUHACXX_AGTCAA_L003_R1.fastq instead of...
Forum: RNA Sequencing 09-25-2014, 07:07 AM
Replies: 10
Views: 3,184
Posted By kopi-o
I think your approach seems sound. By...

I think your approach seems sound.

By "complex" design I mean that there is more than one experimental factor that varies. For example, let's say you are looking at RNA-seq of tumor and paired...
Forum: RNA Sequencing 09-24-2014, 01:12 AM
Replies: 10
Views: 3,184
Posted By kopi-o
That's because there *is* no clear cut answer :) ...

That's because there *is* no clear cut answer :)

- If you have a complex design (more than one experimental factor varies), you want to use limma, edgeR or DESeq2. All reviews tend to agree that...
Forum: Bioinformatics 08-20-2014, 01:32 PM
Replies: 14
Views: 5,580
Posted By kopi-o
Use the DESeqDataSetFromHTSeq function from...

Use the DESeqDataSetFromHTSeq function from DESeq2, or repeatedly use the "join" Unix/Linux command line tool, or use something from this thread
...
Forum: Bioinformatics 08-18-2014, 02:12 AM
Replies: 18
Views: 9,895
Posted By kopi-o
Did you try the design <-...

Did you try the design <- model.matrix(~drug+patientID) mentioned by mikep?

In many (perhaps most) of the analyses I have done of patient RNA-seq data, there are no differentially expressed genes...
Forum: Bioinformatics 07-09-2014, 03:26 AM
Replies: 3
Views: 1,076
Posted By kopi-o
I believe that the PRICE assembler...

I believe that the PRICE assembler (http://derisilab.ucsf.edu/software/price/) is constructed for this use case. You might want to try it. I haven't had time to test it yet, but plan to apply it to a...
Forum: Bioinformatics 07-07-2014, 04:20 PM
Replies: 5
Views: 3,302
Posted By kopi-o
Just use limma. You don't need to do voom().

Just use limma. You don't need to do voom().
Forum: Bioinformatics 06-24-2014, 07:05 AM
Replies: 11
Views: 4,108
Posted By kopi-o
Sure you can. The FPKM values will be in...

Sure you can. The FPKM values will be in genes.fpkm_tracking (and isoforms.fpkm_tracking) after you run Cufflinks. If you are working on hg19 (which you seem to be) it would probably be easier to run...
Forum: RNA Sequencing 06-23-2014, 01:25 PM
Replies: 14
Views: 38,035
Posted By kopi-o
You might want to check out this paper:...

You might want to check out this paper: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0091851
Forum: Sample Prep / Library Generation 05-31-2014, 04:14 PM
Replies: 4
Views: 3,485
Posted By kopi-o
At least review these papers to understand how...

At least review these papers to understand how low RIN might affect quantification and differential expression before you give up hope:

"Sequencing Degraded RNA Addressed by 3' Tag Counting"...
Forum: Illumina/Solexa 05-07-2014, 04:42 AM
Replies: 3
Views: 1,206
Posted By kopi-o
I've heard that in some RNA viruses, the capsid...

I've heard that in some RNA viruses, the capsid protects the viral RNA against RNases, so you can use RNase to deplete non-viral RNA ... but if you don't know what kind of virus it is this might be a...
Forum: Epigenetics 04-01-2014, 02:26 PM
Replies: 3
Views: 2,257
Posted By kopi-o
It's definitely used for that sort of thing. ...

It's definitely used for that sort of thing.

http://scholar.google.se/scholar?q=ChIP-seq+histone+modifications
Forum: Bioinformatics 03-19-2014, 02:05 PM
Replies: 20
Views: 4,897
Posted By kopi-o
I wouldn't use Velvet for metagenomic samples....

I wouldn't use Velvet for metagenomic samples. I'd recommend IDBA-UD or Ray instead. Perhaps Spades too even though that was not develoiped with metagenomics in mind. You might want to give them a...
Forum: Bioinformatics 01-23-2014, 12:44 AM
Replies: 24
Views: 13,926
Posted By kopi-o
Looks very impressive! Can it beat STAR (speed...

Looks very impressive! Can it beat STAR (speed and accuracy wise) for RNA-seq though? (RNA-seq is listed as one of the use cases towards the end)
Forum: RNA Sequencing 12-22-2013, 04:22 PM
Replies: 4
Views: 1,653
Posted By kopi-o
If you have used Cufflinks, you will often find...

If you have used Cufflinks, you will often find such FPKM values for very short transcripts, like miRNAs. Check if that is the case.
Forum: RNA Sequencing 10-09-2013, 04:14 AM
Replies: 4
Views: 2,255
Posted By kopi-o
dpryan's suggestions are good (look out for batch...

dpryan's suggestions are good (look out for batch effects!), but in addition, as you have so many replicates, I would try SAMSeq (samr package in R) which usually works well in such a scenario.
Forum: Bioinformatics 09-27-2013, 05:55 AM
Replies: 3
Views: 1,562
Posted By kopi-o
CistromeMap: http://cistrome.org/pc/ is...

CistromeMap: http://cistrome.org/pc/

is another alternative
Forum: General 09-19-2013, 02:36 PM
Replies: 8
Views: 3,674
Posted By kopi-o
I concur with the last couple of posts - there is...

I concur with the last couple of posts - there is little that you can't do with a desktop/laptop computer. Even assembly does not take that much memory if you use e g Minia.
Forum: Epigenetics 09-18-2013, 01:13 PM
Replies: 10
Views: 6,223
Posted By kopi-o
You could try the genomic association tester:...

You could try the genomic association tester: http://code.google.com/p/genomic-association-tester/
Forum: Bioinformatics 09-18-2013, 08:55 AM
Replies: 10
Views: 3,527
Posted By kopi-o
I would not count on cuffdiff2. Why not try...

I would not count on cuffdiff2. Why not try SAMstrt? The first author of it did extensive tests of different software packages for single-cell data with many replicates and found SAMSeq performed...
Forum: RNA Sequencing 08-27-2013, 12:31 AM
Replies: 3
Views: 2,428
Posted By kopi-o
The purpose of using the transcriptome index is...

The purpose of using the transcriptome index is to increase sensitivity, not necessarily to speed up the run (even though it could do that too, I suppose).

If you want to map RNA-seq reads to the...
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